AlignACE 3.0 10/20/99 AlignACE2 -i PH/PH_operons001_100.orf Parameter values: expect = 10 gcback = 0.38 minpass = 200 seed = 944255112 numcols = 10 undersample = 1 oversample = 1 Input sequences: #0 PH0002 233 155aa long hypothetical transcription termination-antitermination factor #1 PH0092 99 821aa long hypothetical phosphoenolpyruvate synthase #2 PH0397 58 395aa long hypothetical protein #3 PH0398 65 334aa long hypothetical protein #4 PH0399 21 229aa long hypothetical protein #5 PH0627 54 250aa long hypothetical protein #6 PH0628 42 295aa long hypothetical methionyl aminopeptidase #7 PH0974 300 356aa long hypothetical dipeptidase #8 PH1149 89 351aa long hypothetical X-Pro dipeptidase #9 PH1242 48 262aa long hypothetical pseudouridylate synthase #10 PH1483 36 102aa long hypothetical 30S ribosomal protein S10 #11 PHS044 244 82aa long hypothetical DNA-directed RNA polymerase subunit Hprotein #12 PH1641 101 148aa long hypothetical 30S ribosomal protein S13 #13 PH1705 300 342aa long hypothetical protein #14 PH1706 76 411aa long hypothetical translation initiation factor eIF-2 gamma #15 PH1753 77 196aa long hypothetical adenylate kinase #16 PH1754 33 468aa long hypothetical preprotein translocase secY subunit #17 PH1771 194 127aa long hypothetical protein #18 PH1779 139 258aa long hypothetical protein #19 PH1822 94 205aa long hypothetical protein #20 PH1899 284 735aa long hypothetical elongation factor 2 #21 PH1901 118 282aa long hypothetical dehydrogenase #22 PH1902 49 365aa long hypothetical protein Motif 1 AATTCACCCCCCAGATTTTATAGCTCCCAGGG 19 72 0 GGAGAATTGCCCCCCAAAAGTTTTTTAAGATGAAC 11 219 0 TATTCTGGATCCTCCTGGGGTTAGTTCTGTATTAC 7 143 1 CTCGCAACCTCCCGAGATTTATTAAGGATTAA 9 7 1 CCTCCTAAAATTTATTTTTTAGGGT 16 0 1 CCTCCAAGCATTAAAATTCCTATAA 0 218 0 TGGGCGTTTGCCCGCCGGGGTTCAAATCCCCGTCC 12 39 1 CACCGGGGCACCGCCGAAGATTCTTCGAATACAGA 11 37 0 ACGTAATCCCCCGAAATATTTTTACACCAAAT 5 32 0 GCATCTCCTACCCCCACAACTTGATGGTTATTTAA 0 30 0 AAGGTTTCCACCCTCGAAGATTGATAATTCTTAAA 18 41 0 ACCTCCTCGCCTCCAGAAGTGTTTGTTGATCCGT 14 52 0 TGTTGCCCTCCGAGAGATTTTCTTAGACCAA 18 118 0 AGTTATTATCCCTCCAGGCGGTCTTGAATGGCC 7 8 0 AAATTATTATCCTTCAGAATTTTAATAAAAAGGAA 15 16 0 TTAAATCACCCCAAGAATTAAAGAAAAGGGAA 10 14 0 GATTTTATAGCTCCCAGGGTTTTAATACTTTTAAC 19 56 0 TCTTCACCCCTAATCTTACAACCCTGAAAG 15 57 0 GAATGGAGCCCCGGCCGGGCTTTGAACCCGGGACC 11 108 0 GTTTCCCTCCGAGGATATAGCAAGGATCA 20 4 1 TTTATCCCCCTCCAGATTGAGTGAAATTCTGG 12 79 0 TGACATCTAAACTTCTGAACTTCTAATCCCAGGAA 20 211 1 TGTACTCCTCCCATCCGGGCTTCTTCGTTACCAGG 0 117 0 ***** ** ** * MAP Score: 22.7059 Motif 2 ATATTTTAAAAAAACTTTTGCAAAGTAATGAGA 3 24 0 GGAACATTATAAAATTTTTTGAATAAAATAGTT 8 47 0 ATTGCCCCCCAAAAGTTTTTTAAGATGAACATC 11 216 0 TAATTCTTAAAAAATTTTTGCAAAAGCCATAAG 18 19 0 AAAGCCTTTTAAATCTTTTATAAAAACACCACA 18 78 1 GAATTGCTTAAAAGATTTTAAAAAGTTATTTGA 13 253 0 TAATCCCAGGAAAAGCTTTATAACCCTACTTTT 20 234 1 AAAAGATTTAAAAGGCTTTCGAAGGTTTCCACC 18 64 0 GAGTAGCACTAAAATTTTTAACATTATCTTAGG 2 28 0 ATTTAATTTAAAAATTTTAAGAAAAG 0 3 0 TAATCCCCCGAAATATTTTTACACCAAATCAGA 5 28 0 AGAACTCCAGAAAAATTCTTAAATGCTTTAAGA 13 196 1 TTTTTGAATAAAATAGTTTAAAATCCCTATGTA 8 32 0 CCATTCTAATAAATCTTTCGCAAGTAATATAAG 11 137 1 TACAACCCTGAAAGTGTTTAAAATTATTATCCT 15 38 0 AAGTGAGCATAAATATTTATAAACCTAGTTCAA 21 38 0 CTATTCTATAAAAATTTATGGAAAGATTTAGAA 22 19 0 ACTTATATTTAAATACTTCGGAAAAGGAGGAGG 19 24 1 GGAGGAGGTTAAAAGTATTAAAACCCTGGGAGC 19 49 1 CCGTTGGATGAAATGCTCTTTAAAGAAGTCCTA 17 40 1 CAGAACTTAAAAAGGCTTATTAAATTATGAGAA 13 107 1 GCGAGTTCTCAAATTTTTCTTCATCAAATAACT 13 230 1 **** **** ** MAP Score: 20.5372 Motif 3 GAGAATTGCCCCCCAAAAGTTTTTTAAGATGAA 11 220 0 ACCTCCTCGCCTCCAGAAGTGTTTGTTGATCCG 14 53 0 TGTTGCCCTCCGAGAGATTTTCTTAGACCA 18 119 0 ACGTAATCCCCCGAAATATTTTTACACCAA 5 34 0 TAGGAGACCCCCTTTAGTCTT 4 0 0 GTCCATAACTCACCCTAAGTTTTA 1 1 0 TCTCATCGATCCCCTCGATTATTGTCTTGACTT 17 122 0 TTAAATCACCCCAAGAATTAAAGAAAAGG 10 17 0 GATTATAGAACTCCAGAAAAATTCTTAAATGCT 13 190 1 GAGTCACTTGCTCCCGTAGAGTTTGTCGTAGTA 7 241 0 CTCGCAACCTCCCGAGATTTATTAAGGATT 9 7 1 AATCTTACAACCCTGAAAGTGTTTAAAATTATT 15 43 0 GATTTTATAGCTCCCAGGGTTTTAATACTTTTA 19 58 0 GGGTGGAAACCTTCGAAAGCCTTTTAAATCTTT 18 63 1 CTAACCTCCTTGATCTTTGGGAACATTA 8 71 0 AATTCACCCCCCAGATTTTATAGCTCCCA 19 75 0 GAGAACTCGCCTCTTAAAGCATTTAAGAATTTT 13 207 0 CCTCCTAAAATTTATTTTTTAGG 16 0 1 AGGACCACCCCTTAAATGTCTGATTTGGTG 5 7 1 ATACTTTGCTTCTAAATCTTTCCATAAATTT 22 8 1 TCTTCACCCCTAATCTTACAACCCTGA 15 60 0 **** **** ** MAP Score: 17.5471 Motif 4 CCGGGTTCAAAGCCCGGCCGGGGCTCCATTCT 11 112 1 CATATTCTGGATCCTCCTGGGGTTAGTTCTGT 7 141 1 GAAATTCTGGCGCCGGGACGGGGATTTGAACC 12 57 0 CGTGGGCGTTTGCCCGCCGGGGTTCAAATCCC 12 37 1 CCTGATAAGCTTGCTCGGGTTTACTTAAA 20 265 0 GTAACGAAGAAGCCCGGATGGGAGGAGTACAA 0 121 1 TACCAGGCTGAGCCACCGGGGCACCGCCGAAG 11 53 0 AGAATTATCAATCTTCGAGGGTGGAAACCTTC 18 45 1 TCCTTGCTATATCCTCGGAGGGAAAC 20 4 0 CAGATTTTATAGCTCCCAGGGTTTTAATACTT 19 61 0 GAGTAGGATTAGCTTCGAGAGGGATAAAAATA 20 85 1 CATTCAAGACCGCCTGGAGGGATAATAACTGG 7 13 1 CTAAGAAAATCTCTCGGAGGGCAACA 18 123 1 ATTTCACTCAATCTGGAGGGGGATAAA 12 84 1 CTGATTCTTCTGCCATGCGGGGAACTGTTAAT 20 141 1 TATTCGAAGAATCTTCGGCGGTGCCCCGGTGG 11 41 1 GAGCTATAAAATCTGGGGGGTGAATT 19 78 1 GATGCCAGAGTTCCAGGAGAGGGTCAGGAACT 0 60 1 TCCTTAATAAATCTCGGGAGGTTGCGAG 9 6 0 CCGGTGGCTCAGCCTGGTAGAGCGGCCGCTTG 11 66 1 **** ** **** MAP Score: 15.49 Motif 5 CTTGCTATATCCTCGGAGGGAAAC 20 4 0 CCTGGTAGGGCGCGGGCCTT 12 0 1 TAAGAAAATCTCTCGGAGGGCAACA 18 124 1 TTTCACTCAATCTGGAGGGGGATAAA 12 85 1 AACAAACACTTCTGGAGGCGAGGAGGT 14 59 1 GTATTAAAACCCTGGGAGCTATAAAATCTG 19 63 1 GGTGGCTCAGCCTGGTAGAGCGGCCGCTTG 11 68 1 AGCTATAAAATCTGGGGGGTGAATT 19 79 1 TATTCTGGATCCTCCTGGGGTTAGTTCTGT 7 143 1 GGGATTTGAACCCCGGCGGGCAAACGCCCA 12 39 0 AGTTATTATCCCTCCAGGCGGTCTTGAATG 7 13 0 TCGGCGGTGCCCCGGTGGCTCAGCCTGGTA 11 55 1 CCTTAATAAATCTCGGGAGGTTGCGAG 9 7 0 AACGAAGAAGCCCGGATGGGAGGAGTACAA 0 123 1 TTTTTATCCCTCTCGAAGCTAATCCTACTC 20 85 0 AGAGAGTGTTCCTGGTAACGAAGAAGCCCG 0 107 1 AGGTTTCCACCCTCGAAGATTGATAATTCT 18 45 0 AGTCACTTGCTCCCGTAGAGTTTGTCGTAG 7 243 0 GCCTTGAGAGCCCGTGGGCGTTTGCCCGCC 12 25 1 ********** MAP Score: 13.4659 Motif 6 GACCCTCTCCTGGAACTCTGGCATCTCCTACCCCCAC 0 48 0 GATAATACCTCTAATCCCAGGAACGTCAATGAGCTTA 7 78 1 TAATACAGAACTAACCCCAGGAGGATCCAGAATATGA 7 140 0 GAATCTTCGGCGGTGCCCCGGTGGCTCAGCCTGGTAG 11 49 1 CGGCCGGGCTTTGAACCCGGGACCTGCCGCTTACCAA 11 95 0 TTTATTAGAATGGAGCCCCGGCCGGGCTTTGAACCCG 11 113 0 CGCCGGGGTTCAAATCCCCGTCCCGGCGCCAGAATTT 12 51 1 TTAAAAGTATTAAAACCCTGGGAGCTATAAAATCTGG 19 57 1 TTCTGAACTTCTAATCCCAGGAAAAGCTTTATAACCC 20 223 1 * ** *** ** ** MAP Score: 12.382 Motif 7 AGCATACCAACAAGCCCTATGACAAGTATCC 0 179 0 ATGTCCATAACTCACCCTAAGTTTTA 1 5 0 CGCCCCTAAGCAAATCCTAAGATAATGTTAA 2 13 1 TAGATCACCCTAATTCCACGATTTGAAGAT 6 22 0 GATAATACCTCTAATCCCAGGAACGTCAATG 7 78 1 TAATACAGAACTAACCCCAGGAGGATCCAGA 7 146 0 AATACTACGACAAACTCTACGGGAGCAAGTG 7 239 1 TTAAATCACCCCAAGAATTAAAGAA 10 21 0 CCTCTCGAAGCTAATCCTACTCCTTCTATAG 20 76 0 TTCTGAACTTCTAATCCCAGGAAAAGCTTTA 20 223 1 GAAAAGCTTTATAACCCTACTTTTTAAGTAA 20 243 1 ********* * MAP Score: 9.25564 Motif 8 GGTAACGAAGAAGCCCGGATGGGAGGAGTACAAAA 0 120 1 TAAAACTTAGGGTGAGTTATGGACATT 1 2 1 AAGACTAAAGGGGGTCTCCTA 4 0 1 GGCCATTCAAGACCGCCTGGAGGGATAATAACT 7 8 1 ATACAGAACTAACCCCAGGAGGATCCAGAATATGA 7 140 0 ATACTACGACAAACTCTACGGGAGCAAGTGACTCC 7 240 1 GAAAAATATAAAAATTAATCGGAGTCACTTGCTCC 7 260 0 ATCCTTAATAAATCTCGGGAGGTTGCGAG 9 4 0 GTATTCGAAGAATCTTCGGCGGTGCCCCGGTGGCT 11 40 1 CCCGGGTTCAAAGCCCGGCCGGGGCTCCATTCTAA 11 111 1 TTCATCTTAAAAAACTTTTGGGGGGCAATTCTCC 11 220 1 ACGGATCAACAAACACTTCTGGAGGCGAGGAGGT 14 52 1 CTCTTTAAAGAAGTCCTAAAGGAGCAACAGAGAAT 17 55 1 AGTCAAGACAATAATCGAGGGGATCGATGAGAAAG 17 123 1 AAGAATTATCAATCTTCGAGGGTGGAAACCTTCGA 18 44 1 TCTTAGACCAAAGACTGTTGTGGTGTTTTTATAAA 18 94 0 TTGGTCTAAGAAAATCTCTCGGAGGGCAACA 18 118 1 TGGGAGCTATAAAATCTGGGGGGTGAATT 19 75 1 CCTGATAAGCTTGCTCGGGTTTACTTAAAAA 20 263 0 ** *** ***** MAP Score: 6.47005 Motif 9 AATAACCATCAAGTTGTGGGGGTAGGAGATGCCAGAG 0 33 1 TTGGTGTAAAAATATTTCGGGGGATTACGT 5 34 1 GCCATTCAAGACCGCCTGGAGGGATAATAACTGGGAT 7 11 1 AAGAGGTGGCAAGAACTTGGAGAAGAAACTGTAGCCA 7 187 1 ATACTACGACAAACTCTACGGGAGCAAGTGACTCCGA 7 240 1 AATGTTCCCAAAGATCAAGGAGGTTAG 8 72 1 TGGTAAGCGGCAGGTCCCGGGTTCAAAGCCCGGCCGG 11 96 1 TCATCTTAAAAAACTTTTGGGGGGCAATTCTCC 11 221 1 AATTTCACTCAATCTGGAGGGGGATAAA 12 83 1 TCAGGGTTGTAAGATTAGGGGTGAAGA 15 60 1 CCTAAAATTTATTTTTTAGGGTGTTGAGTC 16 13 1 AGTCAAGACAATAATCGAGGGGATCGATGAGAAAGAG 17 123 1 AGAATTATCAATCTTCGAGGGTGGAAACCTTCGAAAG 18 45 1 GGTCTAAGAAAATCTCTCGGAGGGCAACA 18 120 1 AAATACTTCGGAAAAGGAGGAGGTTAAAAGTATTAAA 19 34 1 TGGGAGCTATAAAATCTGGGGGGTGAATT 19 75 1 GAGTAGGATTAGCTTCGAGAGGGATAAAAATAAGATA 20 85 1 * ** ***** ** MAP Score: 5.90118 Motif 10 CCAGAGTTCCAGGAGAGGGTCAGGAACTTTTTCAAGGAGTCGAA 0 64 1 GAACTTTTTCAAGGAGTCGAAGAGAGTGTTCCTGGTAACGAAGA 0 87 1 GTTCCTGGTAACGAAGAAGCCCGGATGGGAGGAGTACAAAAAGG 0 114 1 AGCAAATCCTAAGATAATGTTAAAAATTTTAGTGCTACTCTTTA 2 21 1 CGCTTCAAAGAAGAGGTGGCAAGAACTTGGAGAAGAAACTGTAG 7 177 1 TCAGAATCAAAAGGCGGAGTGTAGATGATGTTCATCTTAAAAAA 11 190 1 TTGAAATTTGAGGAATGGGAGAAGATTGTTTGGAATCATTAAAC 13 11 1 ATACATAGAAAGGGCAAGGTACGGAAAAGTCAAGACAATAATCG 17 96 1 ACAATAATCGAGGGGATCGATGAGAAAGAGTTTGATCTGGAGGA 17 130 1 TTTGATCTGGAGGAAATAGCAAAGAAGCTCAAGGCGAAGTTGGC 17 160 1 ACTTCGGAAAAGGAGGAGGTTAAAAGTATTAAAACCCTGGGAGC 19 38 1 TTTCCCTCCGAGGATATAGCAAGGATCATTCATGAGGCCGTTTT 20 11 1 CCCCTATAGAAGGAGTAGGATTAGCTTCGAGAGGGATAAAAATA 20 73 1 **** * *** * * MAP Score: 4.9104 Motif 11 CTGGTAACGAAGAAGCCCGGATGGGAGGAGTAC 0 118 1 ATAGGAATTTTAATGCTTGGAGG 0 220 1 TAAAACTTAGGGTGAGTTATGGAC 1 1 1 ATAATACCTCTAATCCCAGGAACGTCAATGAGC 7 79 1 AATACAGAACTAACCCCAGGAGGATCCAGAATA 7 143 0 TAATCCTTAATAAATCTCGGGAGGTTGCGAG 9 8 0 CCCTTTTCTTTAATTCTTGGGGTGATTTAA 10 16 1 GGCCGGGCTTTGAACCCGGGACCTGCCGCTTAC 11 98 0 GACGGGGATTTGAACCCCGGCGGGCAAACGCCC 12 40 0 TAAAAGTATTAAAACCCTGGGAGCTATAAAATC 19 58 1 TGGGAGCTATAAAATCTGGGGGGTGAATT 19 75 1 GATCCTTGCTATATCCTCGGAGGGAAAC 20 5 0 TCTGAACTTCTAATCCCAGGAAAAGCTTTATAA 20 224 1 *** *** *** * MAP Score: 4.68484 Motif 12 GTTCCTGGTAACGAAGAAGCCCGGATGGGAGGAGTACA 0 114 1 GGCCATTCAAGACCGCCTGGAGGGATAATAACTG 7 6 1 GAGTCCTCATATTCTGGATCCTCCTGGGGTTAGTTCTG 7 134 1 CGAAGAATCTTCGGCGGTGCCCCGGTGGCTCAGCCTGG 11 45 1 GGCTCAGCCTGGTAGAGCGGCCGCTTGGTAAGCGGCAG 11 71 1 AGATTTATTAGAATGGAGCCCCGGCCGGGCTTTGAACC 11 115 0 TAGGGCGCGGGCCTTGAGAGCCCGTGGGCGTTTGCCCG 12 15 1 CCGGGACGGGGATTTGAACCCCGGCGGGCAAACGCCCA 12 39 0 TTGGTGCCTAGGATAGTAAATCCGTTGGATGAAATGCT 17 19 1 CGGAAAAGTCAAGACAATAATCGAGGGGATCGATGAGA 17 117 1 CTTTGGTCTAAGAAAATCTCTCGGAGGGCAACA 18 116 1 CACCCCCCAGATTTTATAGCTCCCAGGGTTTTAATACT 19 62 0 GAATGATCCTTGCTATATCCTCGGAGGGAAAC 20 4 0 AGGTAGGAATTAACAGTTCCCCGCATGGCAGAAGAATC 20 143 0 CCCTTGATCGTGAACCGATGGGTTTAAGTTGA 21 4 1 * * ***** *** MAP Score: 3.01346 Motif 13 GAACTCTGGCATCTCCTACCCCCACAACTTGATG 0 39 0 CTTTTTGTACTCCTCCCATCCGGGCTTCTTCGTT 0 123 0 CCCCCGAAATATTTTTACACCAAATCAGACATTT 5 23 0 CTAAGATTAAGGCTATTATCCCAGTTATTATCCC 7 31 0 TCGTGATAATACCTCTAATCCCAGGAACGTCAAT 7 74 1 CCTGGCTACAGTTTCTTCTCCAAGTTCTTGCCAC 7 192 0 GAATAAAATAGTTTAAAATCCCTATGTAATAGGG 8 26 0 GCCCCGGCCGGGCTTTGAACCCGGGACCTGCCGC 11 102 0 GGAGAATTGCCCCCCAAAAGTTTTTTA 11 227 0 CCGGGACGGGGATTTGAACCCCGGCGGGCAAACG 12 43 0 ATTTCGTTGAACTTTATCCCCATGTTTAATGATT 13 44 0 TTCACCCCTAATCTTACAACCCTGAAAGTGTTTA 15 51 0 GACTCAACACCCTAAAAAATAAAT 16 19 0 GCTTTCGAAGGTTTCCACCCTCGAAGATTGATAA 18 49 0 GAGGTTAAAAGTATTAAAACCCTGGGAGCTATAA 19 53 1 AATTCACCCCCCAGATTTTATAGC 19 80 0 AAACTTCTGAACTTCTAATCCCAGGAAAAGCTTT 20 219 1 CCCAGGAAAAGCTTTATAACCCTACTTTTTAAGT 20 238 1 * *** ***** * MAP Score: 1.55159 Motif 14 TCTGATTTGGTGTAAAAATATTTCGGGGGATTACGT 5 28 1 GGCCATTCAAGACCGCCTGGAGGGATAATAACT 7 5 1 TGGAGAATACTACGACAAACTCTACGGGAGCAAGTGAC 7 234 1 TTTCTTCCCTTTTCTTTAATTCTTGGGGTGATTTAA 10 10 1 GATGTTCATCTTAAAAAACTTTTGGGGGGCAATTCTCC 11 216 1 GGCGCCAGAATTTCACTCAATCTGGAGGGGGATAAA 12 75 1 TCAAATAACTTTTTAAAATCTTTTAAGCAATTCACGTT 13 253 1 ACTACGGATCAACAAACACTTCTGGAGGCGAGGAGGT 14 49 1 TTCTTCCTTTTTATTAAAATTCTGAAGGATAATAATTT 15 13 1 AGGATAATAATTTTAAACACTTTCAGGGTTGTAAGATT 15 38 1 CCTCCTAAAATTTATTTTTTAGGGTGTTGAGTC 16 6 1 GAAATGCTCTTTAAAGAAGTCCTAAAGGAGCAACAGAG 17 49 1 ATTTTTTAAGAATTATCAATCTTCGAGGGTGGAAACCT 18 37 1 CAGTCTTTGGTCTAAGAAAATCTCTCGGAGGGCAACA 18 112 1 AAACCCTGGGAGCTATAAAATCTGGGGGGTGAATT 19 69 1 * * * *** **** MAP Score: 0.204407